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Unpin biopython and update Bio.Alphabet usage #46

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jaimergp opened this issue Sep 9, 2020 · 0 comments
Open

Unpin biopython and update Bio.Alphabet usage #46

jaimergp opened this issue Sep 9, 2020 · 0 comments
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module-structure-superposition Concerns opencadd.structure.superposition module

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jaimergp commented Sep 9, 2020 •
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Code at opencadd/structure/superposition/sequences.py uses Bio.Alphabet idioms, which have been deprecated as of biopython 1.78. We are pinning to 1.77 now (see #45) but this workaround is not definitive and should be addressed with a code update to stop using Bio.Alphabet.

Details on upgrade paths: https://biopython.org/wiki/Alphabet
@dominiquesydow dominiquesydow added the module-structure-superposition Concerns opencadd.structure.superposition module label Sep 8, 2021
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